Variant report

Variant	rs55777000
Chromosome Location	chr5:58651958-58651959
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10043994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10072637	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10077672	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10514866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11747768	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13356883	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17725522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55697445	1.00[AFR][1000 genomes]
rs57695545	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60958690	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9292202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9292205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9292206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023628	chr5:58557950-58757438	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv1030716	chr5:58636116-58718362	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1032732	chr5:58637179-58689010	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1022160	chr5:58645805-58689010	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58635200-58652600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:58642200-58653200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr5:58642600-58652600	Weak transcription	Fetal Brain Male	brain
4	chr5:58642600-58652600	Weak transcription	Small Intestine	intestine
5	chr5:58643600-58652400	Weak transcription	Fetal Kidney	kidney
6	chr5:58646200-58654400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:58648000-58652600	Weak transcription	Fetal Muscle Leg	muscle
8	chr5:58648000-58654200	Weak transcription	Ovary	ovary
9	chr5:58648200-58652200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr5:58648200-58652200	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr5:58648400-58652400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr5:58648400-58652600	Weak transcription	Brain Hippocampus Middle	brain
13	chr5:58648600-58652200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr5:58648600-58652600	Weak transcription	Brain Angular Gyrus	brain
15	chr5:58648600-58652600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr5:58648600-58653000	Active TSS	Right Ventricle	heart
17	chr5:58648600-58653400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:58648600-58653800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:58649000-58652600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr5:58649000-58652600	Weak transcription	Fetal Stomach	stomach
21	chr5:58649400-58652600	Active TSS	Right Atrium	heart
22	chr5:58649400-58652800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr5:58649400-58653600	Weak transcription	Brain Anterior Caudate	brain
24	chr5:58649400-58653600	Weak transcription	Brain Substantia Nigra	brain
25	chr5:58649400-58654000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr5:58649400-58654200	Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr5:58649600-58653600	Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr5:58650000-58652000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr5:58650000-58652200	Weak transcription	Fetal Lung	lung
30	chr5:58650400-58652600	Weak transcription	Adipose Nuclei	Adipose
31	chr5:58650800-58652400	Weak transcription	Left Ventricle	heart
32	chr5:58651000-58652200	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr5:58651000-58652200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr5:58651000-58653000	Active TSS	Fetal Heart	heart
35	chr5:58651200-58652200	Weak transcription	Rectal Smooth Muscle	rectum
36	chr5:58651400-58652000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr5:58651400-58652000	Active TSS	A549	lung
38	chr5:58651400-58652200	Weak transcription	Psoas Muscle	Psoas
39	chr5:58651400-58652400	Weak transcription	Colon Smooth Muscle	Colon
40	chr5:58651400-58652400	Weak transcription	Stomach Mucosa	stomach
41	chr5:58651400-58652800	Weak transcription	HUVEC	blood vessel
42	chr5:58651400-58653200	Active TSS	Primary B cells from cord blood	blood

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